extract_ss_motif: Extract Splice Site Motifs for MaxEntScan Analysis (5' or 3')

In GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

Extract Splice Site Motifs for MaxEntScan Analysis (5' or 3')

Description

Extracts donor (5') or acceptor (3') splice site motifs from a genomic dataset using BSgenome sequences.

Usage

extract_ss_motif(input, genome, type, verbose, save_fasta, output_file)

Arguments

input	A data frame with columns: seqnames, strand, intron_start, intron_end, transcript_id, intron_number.
genome	A BSgenome object (e.g., from BSgenome.Hsapiens.UCSC.hg38).
type	One of "5ss" (donor) or "3ss" (acceptor).
verbose	Logical; print progress messages.
save_fasta	Logical; write a FASTA file of extracted motifs.
output_file	Name/path of the output FASTA file.

Value

A data frame including extracted splice site motifs.

See Also

assign_splice_sites, df_to_fasta

Examples

## Not run: 
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
  genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
  file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
  gtf_v1 <- load_file(file_v1)
  introns <- extract_introns(gtf_v1)
  motifs_df <- extract_ss_motif(introns, genome, "5ss", verbose = FALSE)
}

## End(Not run)

GencoDymo2 documentation built on Aug. 21, 2025, 5:54 p.m.